<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
<!--Proposed Tool Section: [Targeted Experiments]-->
<tool id="OpenSwathRewriteToFeatureXML" name="OpenSwathRewriteToFeatureXML" version="2.1.0">
  <description>Combines featureXML and mProphet tsv to FDR filtered featureXML.</description>
  <macros>
    <token name="@EXECUTABLE@">OpenSwathRewriteToFeatureXML</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>OpenSwathRewriteToFeatureXML

#if $param_csv:
  -csv $param_csv
#end if
#if $param_featureXML:
  -featureXML $param_featureXML
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_FDR_cutoff:
  -FDR_cutoff $param_FDR_cutoff
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_csv" type="data" format="tabular" optional="True" label="mProphet tsv output file: &quot;all_peakgroups.xls&quot;" help="(-csv) "/>
    <param name="param_featureXML" type="data" format="featurexml" optional="False" label="input featureXML file" help="(-featureXML) "/>
    <param name="param_FDR_cutoff" type="float" value="-1.0" label="FDR cutoff (" help="(-FDR_cutoff) e.g. to remove all features with a an m_score above 0.05 use 0.05 here)"/>
    <expand macro="advanced_options">
      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="featurexml"/>
  </outputs>
  <help>Combines featureXML and mProphet tsv to FDR filtered featureXML.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/doxygen/parameters/output/TOPP_OpenSwathRewriteToFeatureXML.html</help>
</tool>